Where is the startup file stored?
The configuration files are:

startup.blend and userpref.blend, bookmarks.txt, recent-files.txt, 

Windows

The following files are stored in:

%APPDATA%\Blender Foundation\Blender\2.73\config


(%APPDATA% points to C:\Users\&lt;UserName&gt;\AppData\Roaming)

In more recent versions of Windows it will be in: 

C:\Users\&lt;UserName&gt;\AppData\Roaming\Blender Foundation\Blender\&lt;VersionNumber&gt;\config


Note that AppData is a hidden folder, you can change directory to AppData from the command line.

Linux

The Linux versions stores the same files at this path

/home/&lt;UserName&gt;/.config/blender/2.73/config


OS X

For OS X, the config files can be located at 

/Users/&lt;UserName&gt;/Library/Application Support/Blender/2.73/config


The Library folder is also likely to be hidden by default so you may have to look up how to unhide it.

More info: https://www.blender.org/manual/en/getting_started/installing/configuration/directories.html